bowtie
Software Description
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
Info
Module Name
bowtie
Last Updated On
10/23/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
Software Description
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
General Linux
To run this software interactively in a Linux environment run the commands:
module load bowtie
bowtie ...
For bowtie versions 2.0 and above, use the program "bowtie2" instead of simply "bowtie".
To see a list of available options, type the command
bowtie2 -h
Pre-built bowtie indexes for popular genomes are available at
/project/db/genomes/[species]/[build]/bowtie2
Bowtie programs may also be submitted to a queue using PBS script such as the one below:
#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe
#PBS -M sample_email@umn.edu
module load bowtie
bowtie2 -p $PBS_NP reads/e_coli_10000snp.fq ec_snp.sam
Note the use of -p $PBS_NP; this option is used to specify the number of threads used by Bowtie. Also note that only 0.X versions of Bowtie are available on Itasca and Cascade.
Compatibility issues: Bowtie genome indexes built using 0.X versions are not compatible with indexes built using 2.X versions. Significant changes (improvements) have been made to Bowtie command-line options, and to how Bowtie performs alignments. To see a list of installed Bowtie versions type the command
module show bowtie
Bowtie 0.X genome indexes are available at
/project/db/genomes/[SPECIES]/[BUILD]/bowtie
Agate Modules
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2.3.4.1
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1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4
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2.3.4.1
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2.3.4.1
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1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4